LXL04_004942 | RubberDandelionOmics

Gene overview

LXL04_004942

Reference: OH-1004 Chr: Chr01 Coordinates: 150660631-150662280 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1026 bp · LXL04_004942|LXL04_004942|OH1004|cDNA

ATGATGTTAGACCTCAATCTGAATCTTCACCAGAGCGATTTGAGGCCGAATTATGTGACTGACGACGGAGGTAAGTTGGAATACTCTGATGATGTCACCTGGAATTCCTCCGCCGTTAATGTGGAGACAGCTAGCAACGCCGGAGACGACGAGAACACTTACGCTTGCTCGAATCTCGAGTATGCGTTTGACATACTTAAACGAAATAATCTAGAAGACGATAAGAGCGCAACGAAGCAGCTCTTCTCTGAGGTTGGTGA...

CDS

Download CDS FASTA

1026 bp · LXL04_004942|LXL04_004942|OH1004|CDS

ATGATGTTAGACCTCAATCTGAATCTTCACCAGAGCGATTTGAGGCCGAATTATGTGACTGACGACGGAGGTAAGTTGGAATACTCTGATGATGTCACCTGGAATTCCTCCGCCGTTAATGTGGAGACAGCTAGCAACGCCGGAGACGACGAGAACACTTACGCTTGCTCGAATCTCGAGTATGCGTTTGACATACTTAAACGAAATAATCTAGAAGACGATAAGAGCGCAACGAAGCAGCTCTTCTCTGAGGTTGGTGA...

Protein

Download Protein FASTA

341 aa · LXL04_004942|LXL04_004942|OH1004|PROTEIN

MMLDLNLNLHQSDLRPNYVTDDGGKLEYSDDVTWNSSAVNVETASNAGDDENTYACSNLEYAFDILKRNNLEDDKSATKQLFSEVGEDSGVRYSNWLDFNGGSAVDGREFIVRQQSYQQQDSQQMKKGRRGPRSRSSQYRGVTFYRRTGRWESHIWDCGKQVYLGGFDTAHAAARAYDQAAIRFRGLNADINFTINHYQEDLKQMNNLTKEELVHVLRRQSSGFSRGSSKYRGVTLHKCGRWEARIGQFLGKKYIYLGLF...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_004942`
TK1151 ID	TkA01G094990
OH-1004 ID	LXL04_004942
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.700
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_004942

Location Chr01:150660631-150662280 (+)

Description Similar to AP2-2: APETALA2-like protein 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

No hit for this species in the current source table.

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0818800`	Probable transcription factor (By similarity).	Two AP2 family genes, supernumerary bract (SNB) and Osindeterminate spikelet 1 (OsIDS1), synergistically control inflorescence architecture and floral meristem establishment in rice.2012 · DOI: 10.1111/j.1365-313x.2011.04804.x OsMADS1 Represses microRNA172 in Elongation of Palea/Lemma Development in Rice.2016 · DOI: 10.3389/fpls.2016.01891
`UniProt: B8AMA9`	Probable transcription factor (By similarity).	No verified direct reference in this release
`UniProt: B8AXC3`	Probable transcription factor (By similarity).	No verified direct reference in this release
`Os05g0121600`	Probable transcription factor (By similarity).	Coexpression analysis identifies Rice Starch Regulator1, a rice AP2/EREBP family transcription factor, as a novel rice starch biosynthesis regulator.2010 · DOI: 10.1104/pp.110.159517
`Os07g0235800`	Probable transcription factor (By similarity).	OsMADS1 Represses microRNA172 in Elongation of Palea/Lemma Development in Rice.2016 · DOI: 10.3389/fpls.2016.01891

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004942 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0010228 vegetative to reproductive phase transition of meristem Biological Process

GO:0010581 regulation of starch biosynthetic process Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

GO:0080050 regulation of seed development Biological Process

GO:2000014 regulation of endosperm development Biological Process

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

KEGG gene cross-reference

dosa:Os07g0235800

osa:4334582

osa:4342787

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.964

Rank 1 · LXL04_004942 · OH-1004

Cytoplasm0.078

Rank 2 · LXL04_004942 · OH-1004

Cell membrane0.026

Rank 3 · LXL04_004942 · OH-1004

Plastid0.020

Rank 4 · LXL04_004942 · OH-1004

Endoplasmic reticulum0.019

Rank 5 · LXL04_004942 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF00847.27AP2138-186 aa

PF00847.27AP2229-276 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004942	`PF00847.27`	AP2	138	186	7.1e-20	71.8
LXL04_004942	`PF00847.27`	AP2	229	276	7.1e-20	71.8

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q84TB5`	Oryza sativa subsp. japonica	APETALA2-like protein 2	76.684%	Swiss-Prot	moderate database homology
`B8AMA9`	Oryza sativa subsp. indica	APETALA2-like protein 2	76.684%	Swiss-Prot	moderate database homology
`B8AXC3`	Oryza sativa subsp. indica	APETALA2-like protein 1	73.529%	Swiss-Prot	moderate database homology
`Q2TQ34`	Oryza sativa subsp. japonica	APETALA2-like protein 1	73.529%	Swiss-Prot	moderate database homology
`Q8H443`	Oryza sativa subsp. japonica	APETALA2-like protein 3	78.453%	Swiss-Prot	moderate database homology

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